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Detailed information for vg1015866435:

Variant ID: vg1015866435 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 15866435
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.67, T: 0.33, others allele: 0.00, population size: 213. )

Flanking Sequence (100 bp) in Reference Genome:


TCAAGAACAGGAGTTGCTCAGATTGGTGGTTCAGCTACTGGAAGCAGCGCAGCAGAAACCAGGTCGCCGGGTAGCGCCAGCAGAGAAGAAAGCGTTTCAC[C/T]
GGAGGAAACACATGATTTTATGCATGGTCCTGTGCAGTCTCAGTTTTCTATTGGTGCAGCTGGCGCAGGAAATGATGATGGTTCACCAGTGCTACGTGAC

Reverse complement sequence

GTCACGTAGCACTGGTGAACCATCATCATTTCCTGCGCCAGCTGCACCAATAGAAAACTGAGACTGCACAGGACCATGCATAAAATCATGTGTTTCCTCC[G/A]
GTGAAACGCTTTCTTCTCTGCTGGCGCTACCCGGCGACCTGGTTTCTGCTGCGCTGCTTCCAGTAGCTGAACCACCAATCTGAGCAACTCCTGTTCTTGA

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 48.20% 41.60% 3.41% 6.81% NA
All Indica  2759 43.10% 55.90% 0.43% 0.54% NA
All Japonica  1512 66.50% 4.40% 9.19% 19.91% NA
Aus  269 5.20% 94.40% 0.37% 0.00% NA
Indica I  595 25.70% 73.90% 0.00% 0.34% NA
Indica II  465 34.00% 64.70% 0.65% 0.65% NA
Indica III  913 56.30% 43.00% 0.33% 0.33% NA
Indica Intermediate  786 46.30% 52.00% 0.76% 0.89% NA
Temperate Japonica  767 96.30% 1.20% 0.13% 2.35% NA
Tropical Japonica  504 18.50% 6.20% 25.79% 49.60% NA
Japonica Intermediate  241 71.80% 11.20% 3.32% 13.69% NA
VI/Aromatic  96 28.10% 69.80% 2.08% 0.00% NA
Intermediate  90 48.90% 36.70% 7.78% 6.67% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1015866435 C -> T LOC_Os10g30510.1 missense_variant ; p.Pro301Leu; MODERATE nonsynonymous_codon ; P301L Average:44.253; most accessible tissue: Zhenshan97 root, score: 58.674 unknown unknown DELETERIOUS 0.01
vg1015866435 C -> DEL LOC_Os10g30510.1 N frameshift_variant Average:44.253; most accessible tissue: Zhenshan97 root, score: 58.674 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1015866435 NA 4.17E-12 mr1248 Jap_All YES Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1015866435 NA 2.33E-06 mr1425 Jap_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1015866435 NA 4.43E-06 mr1530 Jap_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1015866435 NA 2.20E-07 mr1815 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1015866435 NA 1.71E-08 mr1471_2 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1015866435 NA 3.29E-07 mr1808_2 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251